US2008319677A1PendingUtilityA1
Systems and Methods for Designing Molecules with Affinity for Therapeutic Target Proteins
Est. expiryMay 24, 2027(~0.9 yrs left)· nominal 20-yr term from priority
Inventors:Peter Hrnciar
G16B 15/30G16B 35/20G16C 20/64G16C 20/50G16B 35/00G16B 15/00G16C 20/60
67
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Cited by
0
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Claims
Abstract
The present invention provides methods for designing molecules with affinity for target proteins. More particularly, the present invention provides systems and methods for docking fragment molecules to target protein binding sites. The systems and methods are useful for designing active molecules in drug discovery. Methods of this invention can be implemented in a computer system and may be embodied as computer code in a computer readable medium.
Claims
exact text as granted — not AI-modified1 . A method for designing a molecule with affinity for a target protein, comprising evaluating a position of a fragment molecule relative to a field of distribution densities on a three-dimensional target protein structure.
2 . The method of claim 1 , wherein evaluating the position of the fragment molecule relative to a field of distribution densities on the three-dimensional target protein structure comprises the steps of:
a) obtaining three-dimensional coordinates for each atom in the fragment molecule; b) determining a set of translational and rotational geometric parameters for an initial placement of the fragment molecule in the target protein binding site structure; c) determining a new set of translational and rotational geometric parameters, wherein the new set of translational and rotational geometric parameters is determined by maximizing an overlap between atom positions of the fragment molecule and the field of distribution densities; d) evaluating the fragment molecule-target protein complex geometry; e) modifying the fragment molecule; f) determining a set of translational and rotational geometric parameters for an initial placement of the modified fragment molecule in the target protein binding site structure; and g) repeating steps c) and d).
3 . The method of claim 2 , wherein determining a set of translational and rotational geometric parameters for an initial placement of the fragment molecule in the target protein binding site structure is accomplished with a set of randomly selected translational and rotational parameters.
4 . The method of claim 2 , wherein determining a set of translational and rotational geometric parameters for an initial placement of the fragment molecule in the target protein binding site structure is accomplished with a set of specifically selected translational and rotational parameters.
5 . The method of claim 2 , wherein the step of determining a set of translational and rotational geometric parameters for an initial placement of the fragment molecule in the target protein binding site structure comprises the steps of:
a) selecting n atoms in the fragment molecule; b) selecting n specific locations in the target protein binding site; and c) aligning the atoms in the fragment molecule with the corresponding locations in the target protein binding site by rotational and translational movement to minimize the following equation:
I
(
T
,
R
)
=
∑
j
=
1
n
Mj
-
Aj
wherein T is a translation vector; R is a rotation 3×3 matrix; I(T,R) represents the position of the fragment molecule in the binding site given by translational and rotational geometric parameters; n is the number of selected atoms in the fragment molecule; Mj is a vector defining a position of the distribution density maximum j; and Aj is a vector defining the position of the corresponding atom j in the fragment molecule.
6 . The method of claim 2 , wherein the step of determining a set of translational and rotational geometric parameters for an initial placement of the modified fragment molecule in the target protein binding site structure comprises the steps of:
a) selecting n atoms in the modified fragment molecule; b) selecting n specific locations in the target protein binding site; and c) aligning the atoms in the modified fragment molecule with the corresponding locations in the target protein binding site by rotational and translational movement to minimize the following equation:
I
(
T
,
R
)
=
∑
j
=
1
n
Aj
-
Aj
′
where T is a translation vector; R is a rotation 3×3 matrix; I(T,R) represents the position of the fragment molecule in the binding site given by translational and rotational geometric parameters; n is number of corresponding atoms in the original and modified fragment considered during the placement of the modified fragment; Aj is a vector defining a position of the atom j in the original fragment; and Aj′ is a vector defining the position of the corresponding atom j in the modified fragment.
7 . The method of claim 2 , wherein the step of determining the new set of translational and rotational geometric parameters comprises the steps of:
a) determining distribution density factors Q i for locations of atoms i in docked molecule; and b) calculating a position of the fragment molecule in the target protein binding site I(T,R,B).
8 . The method of claim 7 , wherein the position of the fragment molecule in the target protein binding site is calculated according to the following equation:
I
(
T
,
R
,
B
)
=
∑
i
=
1
n
CQ
i
wherein n is the number of atoms in the fragment molecule; Q i is the distribution density factor at location of the i th atom in a fragment molecule; I(T,R,B) represents the position of the fragment molecule in the binding site given by translational (T), rotational (R), and rotatable bond parameters (B); and C is the proportionality constant for the atom type.
9 . The method of claim 7 , wherein the position of the fragment molecule in the target protein binding site is calculated according to the following equation:
I
(
T
,
R
,
B
)
=
∑
i
=
1
n
CQ
i
F
i
wherein n is the number of atoms in the fragment molecule; Q i is the distribution density factor at location of the i th atom in a fragment molecule; I(T,R,B) represents the position of the fragment molecule in the binding site given by translational (T), rotational (R), and rotatable bond parameters (B); C is the proportionality constant for the atom type; and F i represents the proportion of atom's surface proportion in the contact with the protein surface.
10 . The method of claim 7 , wherein the position of the fragment molecule in the target protein binding site is calculated according to the following equation:
I
(
T
,
R
,
B
)
=
∑
i
=
1
n
CD
i
wherein n is the number of atoms in the fragment molecule; D i is the distance between i th atom in the fragment molecule and a respective local distribution density maximum maximum; I(T,R,B) represents the position of a ligand in a binding site given by translational (T), rotational (R), and rotatable bond parameters (B); and C is the proportionality constant for the atom type.
11 . The method of claim 7 , wherein the position of the fragment molecule in the target protein binding site is calculated according to the following equation:
I
(
T
,
R
,
B
)
=
∑
i
=
1
n
CD
i
F
i
wherein n is the number of atoms in the fragment molecule; D i is the distance between i th atom in the fragment molecule and a respective local distribution density maximum maximum; I(T,R,B) represents the position of a ligand in a binding site given by translational (T), rotational (R), and rotatable bond parameters (B); C is the proportionality constant for the atom type; and F i represents the proportion of atom's surface proportion in the contact with the protein surface.
12 . The method of claim 2 , wherein the step of evaluating the fragment molecule-target protein complex geometry comprises calculating a score according to the position of the fragment molecule relative to a field of distribution densities of the target protein structure, according to the following equation:
Score
=
∑
i
=
1
n
C
*
Q
i
Q
wherein Q i is a distribution density factor or any other measure of occurrence frequency of the atom type at its location or at the location of the nearest grid point in the binding site; Q is the optimal distribution density factor or any other measure of occurrence frequency for the atom type; C is the proportionality constant for the atom type; and n is the number of atoms in the fragment molecule.
13 . The method of claim 12 , further comprising the step of comparing the score to a score threshold value.
14 . The method of claim 2 , wherein the step of evaluating the fragment molecule-target protein complex geometry comprises calculating a distribution density maxima coverage according to the position of the fragment molecule relative to a field of distribution densities of the target protein structure, according to the following equations:
DDMC
Total
=
CM
Total
TM
Total
×
100
DDMC
HD
=
CM
HD
TM
HD
×
100
DDMC
HA
=
CM
HA
TM
HA
×
100
DDMC
AP
=
CM
AP
TM
AP
×
100
where DDMC Total , DDMC HD , DDMC HA , and DDMC AP are total distribution density maxima coverage for all, hydrogen bond donor, hydrogen bond acceptor, and apolar maxima, respectively; CM HD , CM HA , and CM AP are number of covered distribution density maxima for hydrogen bond donor, hydrogen bond acceptor, and apolar types, respectively; and TM HD , TM HA , and TM AP are total number of considered distribution density maxima for hydrogen bond donor, hydrogen bond acceptor, and apolar types, respectively.
15 . The method of claim 14 , wherein the step of evaluating the fragment molecule-target protein complex geometry comprises calculating a relative distribution density maxima coverage according to the position of the fragment molecule relative to a field of distribution densities of the target protein structure, according to the following equations:
DDMC
Total
′
=
CM
Total
(
Fragment
)
TM
Total
(
NativeLigand
)
×
100
DDMC
HD
′
=
DDMC
HD
(
Fragment
)
DDMC
HD
(
NativeLigand
)
×
100
DDMC
HA
′
=
DDMC
HA
(
Fragment
)
DDMC
HA
(
NativeLigand
)
×
100
DDMC
AP
′
=
DDMC
AP
(
Fragment
)
DDMC
AP
(
NativeLigand
)
×
100
where DDMC′ Total , DDMC′ HD , DDMC′ HA , and DDMC′ AP represent fragment's relative distribution density maxima coverage for all, hydrogen bond donor, hydrogen bond acceptor, and apolar maxima, respectively.
16 . The method of claim 14 , further comprising the step of comparing the distribution density maxima coverage to a distribution density maxima coverage threshold value.
17 . The method of claim 15 , further comprising the step of comparing the relative distribution density maxima coverage to a relative distribution density maxima coverage threshold value.
18 . The method of claims 1 or 2 , wherein the target protein is selected from the group consisting of Raf kinase, Rho kinase, NF-κB, VEGF receptor kinase, JAK-3, CDK2, FLT-3, EGFR kinase, PKA, p21-activated kinase, MAPK, JNK, AMPK, phosphodiesterase PDE4, Abl kinase, phosphodiesterase PDE5, ADAM33, HIV-1 protease, HIV integrase, RSV integrase, XIAP, thrombin, tissue type plasminogen activator, matrix metalloproteinase, beta secretase, src kinase, fyn kinase, lyn kinase, ZAP-70 kinase, ERK-1, p38 MAPK, CDK4, CDK5, GSK-3, KIT kinase, FLT-1, FLT-4, KDR kinase, and COT kinase.
19 . A system for discovering a molecule with a binding affinity toward a protein target comprising: a processor; and a memory in electrical communication with the processor, wherein the processor is configured to carry out the method of claim 1 .
20 . A computer system comprising: a processor and a memory in electrical communication with the processor, wherein the memory has stored therein data indicative of a three-dimensional target protein binding site representation, comprising the binding site data set produced according to a method comprising the steps of:
a) obtaining three-dimensional coordinates for each atom in the fragment molecule; b) determining a set of translational and rotational geometric parameters for an initial placement of the fragment molecule in the target protein binding site structure; c) determining a new set of translational and rotational geometric parameters, wherein the new set of translational and rotational geometric parameters is determined by maximizing an overlap between atom positions of the fragment molecule and the field of distribution densities; d) evaluating the fragment molecule-target protein complex geometry; e) modifying the fragment molecule; f) determining a set of translational and rotational geometric parameters for an initial placement of the modified fragment molecule in the target protein binding site structure; and g) repeating steps c) and d).
21 . A computer readable medium having computer readable program code embodied therein, wherein the computer readable program code causes the computer to carry out the method comprising the steps of:
a) obtaining three-dimensional coordinates for each atom in the fragment molecule; b) determining a set of translational and rotational geometric parameters for an initial placement of the fragment molecule in the target protein binding site structure; c) determining a new set of translational and rotational geometric parameters, wherein the new set of translational and rotational geometric parameters is determined by maximizing an overlap between atom positions of the fragment molecule and the field of distribution densities; d) evaluating the fragment molecule-target protein complex geometry; e) modifying the fragment molecule; f) determining a set of translational and rotational geometric parameters for an initial placement of the modified fragment molecule in the target protein binding site structure comprising the steps of:
a) selecting n atoms in the fragment molecule;
b) selecting n specific locations in the target protein binding site; and
c) aligning the atoms in the fragment molecule with the corresponding locations in the target protein binding site by rotational and translational movement to minimize the following equation:
I
(
T
,
R
)
=
∑
j
=
1
n
Mj
-
Aj
wherein T is a translation vector; R is a rotation 3×3 matrix; I(T,R) represents the position of the fragment molecule in the binding site given by translational and rotational geometric parameters; n is the number of selected atoms in the fragment molecule; Mj is a vector defining a position of the distribution density maximum j; and Aj is a vector defining the position of the corresponding atom j in the fragment molecule; and
g) repeating steps c) and d).
22 . A computer program product comprising a computer usable medium having computer readable program code comprising computer instructions to a method comprising the steps of:
a) obtaining three-dimensional coordinates for each atom in the fragment molecule; b) determining a set of translational and rotational geometric parameters for an initial placement of the fragment molecule in the target protein binding site structure; c) determining a new set of translational and rotational geometric parameters, wherein the new set of translational and rotational geometric parameters is determined by maximizing an overlap between atom positions of the fragment molecule and the field of distribution densities; d) evaluating the fragment molecule-target protein complex geometry, comprising calculating a distribution density maxima coverage according to the position of the fragment molecule relative to a field of distribution densities of the target protein structure, according to the following equations:
DDMC
Total
=
CM
Total
TM
Total
×
100
DDMC
HD
=
CM
HD
TM
HD
×
100
DDMC
HA
=
CM
HA
TM
HA
×
100
DDMC
AP
=
CM
AP
TM
AP
×
100
where DDMC Total , DDMC HD , DDMC HA , and DDMC AP are total distribution density maxima coverage for all, hydrogen bond donor, hydrogen bond acceptor, and apolar maxima, respectively; CM HD , CM HA , and CM AP are number of covered distribution density maxima for hydrogen bond donor, hydrogen bond acceptor, and apolar types, respectively; and TM HD , TM HA , and TM AP are total number of considered distribution density maxima for hydrogen bond donor, hydrogen bond acceptor, and apolar types, respectively;
e) modifying the fragment molecule;
f) determining a set of translational and rotational geometric parameters for an initial placement of the modified fragment molecule in the target protein binding site structure; and
g) repeating steps c) and d).
23 . A method executed by a computer under the control of a program, said computer including a memory for storing said program, said method comprising the steps of the method of claim 15 .
24 . A computer implemented method for modeling a target protein binding site for determining a candidate molecule's ability to binding to the target protein binding site, comprising the steps of the method of claim 17 .Cited by (0)
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